scholarly journals The colors of life: an interdisciplinary artist-in-residence project to research fungal pigments as a gateway to empathy and understanding of microbial life

2022 ◽  
Vol 9 (1) ◽  
Author(s):  
Sunanda Sharma ◽  
Vera Meyer

Abstract Background Biological pigmentation is one of the most intriguing traits of many fungi. It holds significance to scientists, as a sign of biochemical metabolism and organism-environment interaction, and to artists, as the source of natural colors that capture the beauty of the microbial world. Furthermore, the functional roles and aesthetic appeal of biological pigmentation may be a path to inspiring human empathy for microorganisms, which is key to understanding and preserving microbial biodiversity. A project focused on cross-species empathy was initiated and conducted as part of an artist-in-residence program in 2021. The aim of this residency is to bridge the current divide between science and art through interdisciplinary practice focused on fungi. Results The residency resulted in multiple products that are designed for artistic and scientific audiences with the central theme of biological pigmentation in fungi and other microorganisms. The first product is a video artwork that focuses on Aspergillus niger as a model organism that produces melanin pigment in a biosynthetic process similar to that of humans. The growth and morphology of this commonplace organism are displayed through video, photo, animation, and time-lapse footage, inviting the viewer to examine the likenesses and overlaps between humans and fungi. The second product is The Living Color Database, an online compendium of biological colors for scientists, artists, and designers. It links organisms across the tree of life, focusing on fungi, bacteria, and archaea, and the colors they express through biological pigmentation. Each pigment is represented in terms of its chemistry, its related biosynthesis, and its color expressions according to different indices: HEX, RGB, and Pantone. It is available at color.bio. Conclusions As fungal biotechnology continues to mature into new application areas, it is as important as ever that there is human empathy for these organisms to promote the preservation and appreciation of fungal biodiversity. The products presented here provide paths for artists, scientists, and designers to understand microorganisms through the lens of color, promoting interspecies empathy through research, teaching, and practice.

2020 ◽  
Author(s):  
Daniel León-Periñán ◽  
Alfonso Fernández-Álvarez

ABSTRACTAs one of the main events occurring during meiotic prophase, the dynamics of meiotic chromosome movement is not yet well understood. Currently, although it is well-established that chromosome movement takes an important role during meiotic recombination promoting the pairing between homologous chromosomes and avoiding excessive chromosome associations, it is mostly unclear whether those movements follow a particular fixed pattern, or are stochastically distributed. Using Schizosaccharomyces pombe as a model organism, which exhibits dramatic meiotic nuclear oscillations, we have developed a computationally automatized statistical analysis of three-dimensional time-lapse fluorescence information in order to characterize nuclear trajectories and morphological patterns during meiotic prophase. This approach allowed us to identify a patterned oscillatory microvariation during the meiotic nuclear motion. Additionally, we showed evidence suggesting that this unexpected oscillatory motif might be due to the detection of persistent DNA damage during the nuclear movement, supporting how the nucleus also regulates its oscillations. Our computationally automatized tool will be useful for the identification of new patterns of nuclear oscillations during gametogenesis.


2020 ◽  
Author(s):  
Eric J.G. Pollitt ◽  
Oliver Carnell ◽  
Egbert Hoiczyk ◽  
Jeffrey Green

AbstractMycobacterium smegmatis spreads over soft agar surfaces by sliding motility, a form of passive motility in which growth and reduction of surface adhesion enable the bacteria to push each other outwards. Hence, sliding motility is mostly associated with round colonies. However, M. smegmatis sliding colonies can also produce long, pointed dendrites. Round sliding colonies were readily reproduced, but our non-round colonies were different from those seen previously. The latter (named digitate colonies) had centimetre-long linear protrusions, containing a central channel filled with a free-flowing suspension of M. smegmatis and solid aggregates. Digitate colonies had both a surface pellicle and an inner biofilm component surrounding a central channel, which sat in a cleft in the agar. Time-lapse microscopy showed that the expansion of the fluid-filled channel enabled the lengthwise extension of the protrusions without any perceptible growth of the bacteria taking place. These observations represent a novel type of sliding motility, named hydraulic sliding, associated with a specialised colony structure and the apparent generation of force by expansion of a liquid core. As this structure requires pellicle formation without an initial liquid culture it implies the presence of an unstudied mycobacterial behaviour that may be important for colonisation and virulence.Originality-Significance StatementThis study is the first to identify a new form of passive motility in the mycobacteria; hydraulic sliding, in which liquid expansion is the cause of motility. This form of motility has so far never been described in bacteria. The study also reveals new ways mycobacteria can form biofilms and colonize complex three-dimensional substrates, aspects of mycobacterial biology that are important for infection, pathogenesis and vaccine development.Author SummaryMycobacterium smegmatis is used as a non-pathogenic model organism for pathogenic mycobacteria. During growth, M. smegmatis can move passively over soft agar surfaces by a process called sliding motility, whereby colony growth directly pushes cells outwards. Although passive, sliding motility is believed to be important in allowing bacteria to colonise surfaces. Sliding motility however does not fully account for how M. smegmatis produces dendritic colonies. We attempted to generate dendritic colonies but found instead that the cells produced colonies that had larger protrusions radiating from them (digitate colonies). Digitate colonies are a previously unobserved phenomenon, in that the bacteria create a biofilm-lined, fluid-filled, pellicle-covered, deep cleft in the agar and move across the surface by the expansion of the contained liquid core of the protrusions. Given the new structure and the new mechanism of expansion we have termed this set of behaviours hydraulic sliding. These observations are important as it is a new variation in the way bacteria can move, generate biofilms (notably mycobacterial pellicle) and colonize complex three-dimensional substrates.


2021 ◽  
Author(s):  
David Scheidweiler ◽  
Ankur Deep Bordoloi ◽  
Pietro de Anna

<p>Predicting dispersal patterns is important to understand microbial life in porous media as soils and sedimentary environments. We studied active and passive dispersal of bacterial cells in porous media characterized by two main pore features: fast channels and dead-end cavities. We combined experiments with microfluidic devices and time-lapse microscopy to track individual bacterial trajectories and measure the breakthrough curves and pore scale bacterial abundance. Escherichia coli cells dispersed more efficiently than the non-motile mutants showing a different retention in the dead-end pores. Our findings highlight the role of diffusion dominated dead-end pores on the dispersal of microorganisms in porous media.</p>


2020 ◽  
Author(s):  
Janos Nagy ◽  
László Tálas ◽  
Márta Novák Hajós ◽  
Csilla Bojté ◽  
Alexandra Kiss ◽  
...  

Abstract The performance of domestic agriculture and the food industry is constantly increasing. Demand for food is growing on the global market, with domestic food export growing by 10% in 2019. However, there are still reserves in exploiting the growth path and transforming it into income. Efficiency, revenue and profit growth of each product line depends on numerous factors; one of the key tools being the monitoring of the production process, getting to know the production environment accurately, data collecting, database building, development of applications that support automated interventions and decisions, and integration the above tools. The fundamental objective goal of the presented research is to approach the research of maize pollen cells as an agriculturally relevant model organism from a new direction, the long-term (Time-Lapse System) microscopic study of the growth dynamics of the pollen germ tube. In the scope of the research, two industrially and agriculturally important aspects taken into account, which also detected digitally: the growth of the maize pollen germ tube and the viability of the pollen. The research can provide a basis for the more accurate understanding and subsequent study of the effects of different biotic and abiotic stress factors on pollen growth, and may open up new possibilities in the field of digital agricultural biotechnology.


2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Anahit Penesyan ◽  
Ian T. Paulsen ◽  
Staffan Kjelleberg ◽  
Michael R. Gillings

AbstractBiofilms are organised heterogeneous assemblages of microbial cells that are encased within a self-produced matrix. Current estimates suggest that up to 80% of bacterial and archaeal cells reside in biofilms. Since biofilms are the main mode of microbial life, understanding their biology and functions is critical, especially as controlling biofilm growth is essential in industrial, infrastructure and medical contexts. Here we discuss biofilms both as collections of individual cells, and as multicellular biological individuals, and introduce the concept of biofilms as unique incubators of diversity for the microbial world.


2020 ◽  
Vol 20 (14) ◽  
pp. 1291-1299
Author(s):  
Sébastien Boutin ◽  
Alexander H. Dalpke

Nature offered mankind the first golden era of discovery of novel antimicrobials based on the ability of eukaryotes or micro-organisms to produce such compounds. The microbial world proved to be a huge reservoir of such antimicrobial compounds which play important functional roles in every environment. However, most of those organisms are still uncultivable in a classical way, and therefore, the use of extended culture or DNA based methods (metagenomics) to discover novel compounds promises usefulness. In the past decades, the advances in next-generation sequencing and bioinformatics revealed the enormous diversity of the microbial worlds and the functional repertoire available for studies. Thus, data-mining becomes of particular interest in the context of the increased need for new antibiotics due to antimicrobial resistance and the rush in antimicrobial discovery. In this review, an overview of principles will be presented to discover new natural compounds from the microbiome. We describe culture-based and culture-independent (metagenomic) approaches that have been developed to identify new antimicrobials and the input of those methods in the field as well as their limitations.


2015 ◽  
Vol 18 (3) ◽  
pp. 663-674 ◽  
Author(s):  
N. Nowik ◽  
P. Podlasz ◽  
A. Jakimiuk ◽  
N. Kasica ◽  
W. Sienkiewicz ◽  
...  

Abstract The zebrafish (Danio rerio) has become known as an excellent model organism for studies of vertebrate biology, vertebrate genetics, embryonal development, diseases and drug screening. Nevertheless, there is still lack of detailed reports about usage of the zebrafish as a model in veterinary medicine. Comparing to other vertebrates, they can lay hundreds of eggs at weekly intervals, externally fertilized zebrafish embryos are accessible to observation and manipulation at all stages of their development, which makes possible to simplify the research techniques such as fate mapping, fluorescent tracer time-lapse lineage analysis and single cell transplantation. Although zebrafish are only 2.5 cm long, they are easy to maintain. Intraperitoneal and intracerebroventricular injections, blood sampling and measurement of food intake are possible to be carry out in adult zebrafish. Danio rerio is a useful animal model for neurobiology, developmental biology, drug research, virology, microbiology and genetics. A lot of diseases, for which the zebrafish is a perfect model organism, affect aquatic animals. For a part of them, like those caused by Mycobacterium marinum or Pseudoloma neutrophila, Danio rerio is a natural host, but the zebrafish is also susceptible to the most of fish diseases including Itch, Spring viraemia of carp and Infectious spleen and kidney necrosis. The zebrafish is commonly used in research of bacterial virulence. The zebrafish embryo allows for rapid, non-invasive and real time analysis of bacterial infections in a vertebrate host. Plenty of common pathogens can be examined using zebrafish model: Streptococcus iniae, Vibrio anguillarum or Listeria monocytogenes. The steps are taken to use the zebrafish also in fungal research, especially that dealing with Candida albicans and Cryptococcus neoformans. Although, the zebrafish is used commonly as an animal model to study diseases caused by external agents, it is also useful in studies of metabolic disorders including fatty liver disease and diabetes. The zebrafish is also a valuable tool as a model in behavioral studies connected with feeding, predator evasion, habituation and memory or lateralized control of behavior. The aim of the present article is to familiarize the reader with the possibilities of Danio rerio as an experimental model for veterinary medicine.


2021 ◽  
Author(s):  
Christelle Leung ◽  
Daphne Grulois ◽  
Luis-Miguel Chevin

Phenotypic plasticity, the ability of a given genotype to produce alternative phenotypes in response to its environment of development, is an important mechanism for coping with variable environments. While the mechanisms underlying phenotypic plasticity are diverse, their relative contributions need to be investigated quantitatively to better understand the evolvability of plasticity across biological levels. This requires relating plastic responses of the epigenome, transcriptome, and organismal phenotype, and how they vary with the genotype. Here we carried out this approach for responses to osmotic stress in Dunaliella salina, a green microalga that is a model organism for salinity tolerance. We compared two strains that show markedly different demographic responses to osmotic stress, and showed that these phenotypic responses involve strain- and environment-specific variation in gene expression levels, but a relative low - but significant - effect of strain x environment interaction. We also found an important genotype effect on the genome-wide methylation pattern, but little contribution from environmental conditions to the latter. However, we did detect a significant marginal effect of epigenetic variation on gene expression, beyond the influence of genetic differences on epigenetic state, and we showed that hypomethylated regions are correlated with higher gene expression. Our results indicate that epigenetic mechanisms are either not involved in the rapid plastic response to environmental change in this species, or involve only few changes in trans that are sufficient to trigger concerted changes in the expression of many genes, and phenotypic responses by multiple traits.


2021 ◽  
Vol 12 ◽  
Author(s):  
Gustavo Caetano-Anollés

Communication is an undisputed central activity of life that requires an evolving molecular language. It conveys meaning through messages and vocabularies. Here, I explore the existence of a growing vocabulary in the molecules and molecular functions of the microbial world. There are clear correspondences between the lexicon, syntax, semantics, and pragmatics of language organization and the module, structure, function, and fitness paradigms of molecular biology. These correspondences are constrained by universal laws and engineering principles. Macromolecular structure, for example, follows quantitative linguistic patterns arising from statistical laws that are likely universal, including the Zipf’s law, a special case of the scale-free distribution, the Heaps’ law describing sublinear growth typical of economies of scales, and the Menzerath–Altmann’s law, which imposes size-dependent patterns of decreasing returns. Trade-off solutions between principles of economy, flexibility, and robustness define a “triangle of persistence” describing the impact of the environment on a biological system. The pragmatic landscape of the triangle interfaces with the syntax and semantics of molecular languages, which together with comparative and evolutionary genomic data can explain global patterns of diversification of cellular life. The vocabularies of proteins (proteomes) and functions (functionomes) revealed a significant universal lexical core supporting a universal common ancestor, an ancestral evolutionary link between Bacteria and Eukarya, and distinct reductive evolutionary strategies of language compression in Archaea and Bacteria. A “causal” word cloud strategy inspired by the dependency grammar paradigm used in catenae unfolded the evolution of lexical units associated with Gene Ontology terms at different levels of ontological abstraction. While Archaea holds the smallest, oldest, and most homogeneous vocabulary of all superkingdoms, Bacteria heterogeneously apportions a more complex vocabulary, and Eukarya pushes functional innovation through mechanisms of flexibility and robustness.


2020 ◽  
Author(s):  
Kohji Hotta ◽  
Delphine Dauga ◽  
Lucia Manni

AbstractCiona robusta (Ciona intestinalis type A), a model organism for biological studies, belongs to ascidians, the main class of tunicates, which are the closest relatives of vertebrates. In Ciona, a project on the ontology of both development and anatomy is ongoing for several years. Its goal is to standardize a resource relating each anatomical structure to developmental stages. Today, the ontology is codified until the hatching larva stage. Here, we present its extension throughout the swimming larva stages, the metamorphosis, until the juvenile stages. For standardizing the developmental ontology, we acquired different time-lapse movies, confocal microscope images and histological serial section images for each developmental event from the hatching larva stage (17.5 hour post fertilization) to the juvenile stage (7 days post fertilization). Combining these data, we defined 12 new distinct developmental stages (from Stage 26 to Stage 37), in addition to the previously defined 26 stages, referred to embryonic development. The new stages were grouped into four Periods named: Adhesion, Tail Absorption, Body Axis Rotation, and Juvenile. To build the anatomical ontology, 203 anatomical entities were identified, defined according to the literature, and annotated, taking advantage from the high resolution and the complementary information obtained from confocal microscopy and histology. The ontology describes the anatomical entities in hierarchical levels, from the cell level (cell lineage) to the tissue/organ level. Comparing the number of entities during development, we found two rounds on entity increase: in addition to the one occurring after fertilization, there is a second one during the Body Axis Rotation Period, when juvenile structures appear. Vice versa, one-third of anatomical entities associated with the embryo/larval life were significantly reduced at the beginning of metamorphosis. Data was finally integrated within the web-based resource “TunicAnatO”, which includes a number of anatomical images and a dictionary with synonyms. This ontology will allow the standardization of data underpinning an accurate annotation of gene expression and the comprehension of mechanisms of differentiation. It will help in understanding the emergence of elaborated structures during both embryogenesis and metamorphosis, shedding light on tissue degeneration and differentiation occurring at metamorphosis.


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